RetrogeneDB ID: retro_vpac_39

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1152:748107..748353(+)
• Located in intron of: ENSVPAG00000006596

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NDUFB1
• Ensembl ID: ENSVPAG00000003502
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa [Source:HGNC Symbol;Acc:7695]

Sequence

>retro_vpac_39
CCGGCGCTGCTGGCTGGGCTTGCTGCTGCCCTTGCTTGTGGACTCGTTGTTGGCTCCGAGGCCGCAGCATTCATGCTGAG
CTTACTCCAGGTTGTGCATGACCACTGGGTATGTATACTTGTCCCTGTGGGTGTTGTCTTTGGATGGTATCTAGACAGAA
AGAATGAAGAAAATCTCACTGCCTTCCAGAACAAGAATCTCTTATTTAAAAGGGAATTGATGCCCAATGAAGAAGTCACC
TGGAAG

Alignment

ORF - retro_vpac_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 78.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAPLAGLAAALALGVVVTSEAAAFMMSLLQVVRDHWVHILVPMGFVFGWYLDKKNDEKLTAFRNESLLFK
          PA.LAGLAAALA.G.VV.SEAAAFM.SLLQVV.DHWV.ILVP.G.VFGWYLD.KN.E.LTAF.N..LLFK
Retrocopy PALLAGLAAALACGLVVGSEAAAFMLSLLQVVHDHWVCILVPVGVVFGWYLDRKNEENLTAFQNKNLLFK

Parental  RELRPREEVTWK
          REL.P.EEVTWK
Retrocopy RELMPNEEVTWK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_39 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_39 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014837	1 retrocopy	retro_amel_1060,
Callithrix jacchus	ENSCJAG00000018067	5 retrocopies	retro_cjac_1027, retro_cjac_1053, retro_cjac_1330, retro_cjac_2586, retro_cjac_3294,
Homo sapiens	ENSG00000183648	2 retrocopies	retro_hsap_2646, retro_hsap_311,
Macaca mulatta	ENSMMUG00000022428	2 retrocopies	retro_mmul_1520, retro_mmul_538,
Nomascus leucogenys	ENSNLEG00000017129	1 retrocopy	retro_nleu_652,
Ochotona princeps	ENSOPRG00000012731	2 retrocopies	retro_opri_22, retro_opri_992,
Pongo abelii	ENSPPYG00000006076	1 retrocopy	retro_pabe_2325,
Pan troglodytes	ENSPTRG00000006649	2 retrocopies	retro_ptro_1782, retro_ptro_253,
Pteropus vampyrus	ENSPVAG00000015319	1 retrocopy	retro_pvam_642,
Tursiops truncatus	ENSTTRG00000008130	2 retrocopies	retro_ttru_1515, retro_ttru_830,
Vicugna pacos	ENSVPAG00000003502	2 retrocopies	retro_vpac_257, retro_vpac_39 ,